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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MANOR Resource Report Resource Website 10+ mentions |
MANOR (RRID:SCR_001305) | MANOR | software resource | Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments. | copy number variation, data import, microarray, preprocessing, quality control, two channel, comparative genomic hybridization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02028 | SCR_001305 | CGH Micro-Array NORmalization | 2026-09-19 12:49:40 | 17 | |||||||
|
dyebias Resource Report Resource Website |
dyebias (RRID:SCR_001308) | dyebias | software resource | Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias. | microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:17623705 | GNU General Public License, v3 | biotools:dyebias, OMICS_02025 | https://bio.tools/dyebias | SCR_001308 | dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias | 2026-09-19 12:49:38 | 0 | |||||
|
limmaGUI Resource Report Resource Website 10+ mentions |
limmaGUI (RRID:SCR_001306) | limmaGUI | software resource | Software package for a Graphical User Interface for the limma Microarray package. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15297296 | Free, Available for download, Freely available | OMICS_02027, biotools:limmagui | https://bio.tools/limmagui | SCR_001306 | limmaGUI - GUI for limma package | 2026-09-19 12:49:38 | 14 | |||||
|
ffpe Resource Report Resource Website 500+ mentions |
ffpe (RRID:SCR_001307) | ffpe | software resource | Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). | formalin-fixed, paraffin-embedded, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02026, biotools:ffpe | https://bio.tools/ffpe | SCR_001307 | ffpe - Quality assessment and control for FFPE microarray expression data | 2026-09-19 12:49:38 | 524 | ||||||
|
SeqScape Software Resource Report Resource Website 500+ mentions |
SeqScape Software (RRID:SCR_001604) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. A resequencing package designed for mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification and sequence confirmation. | mutation, sequencing, thermofisher scientific, snp, pathogen sub-typing | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01819 | http://www.thermofisher.com/order/catalog/product/4327091 | SCR_001604 | 2026-09-19 12:49:43 | 543 | ||||||||
|
Clustal Omega Resource Report Resource Website 10000+ mentions |
Clustal Omega (RRID:SCR_001591) | Clustal Omega, Clustalo | alignment software, data processing software, image analysis software, service resource, software application, software resource | Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF. | multiple, sequence, alignment, DNA, RNA, protein, generate, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clustal W2 is related to: Clustal W2 is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:21988835 PMID:20439314 DOI:10.1038/msb.2011.75 |
Free, Available for download, Freely available | OMICS_00972, SCR_016062, biotools:clustalo, nlx_153836 | https://sources.debian.org/src/clustalo/, http://www.clustal.org/omega/, http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-multialign, https://bio.tools/clustalo, https://sources.debian.org/src/clustalo/ | SCR_001591 | 2026-09-19 12:49:44 | 10580 | |||||
|
TileMap Resource Report Resource Website 1+ mentions |
TileMap (RRID:SCR_001589) | algorithm resource, data analysis software, data processing software, software application, software resource, source code | Software tool for microarray tile mapping. It utilizes ChIP-chip peak calling to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest. | microarray, rna, dna, sequencing, chip, tiling, chip-chip peak calling, transcription, binding |
is listed by: OMICtools works with: CisGenome |
PMID:16046496 | Free, Available for download, Freely available | OMICS_00812 | SCR_001589 | tilemapv2, TileMap Version 2 | 2026-09-19 12:49:43 | 8 | |||||||
|
asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | data analysis software, data processing software, software application, software resource, source code | Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq | r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bioconductor has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21838806 | Free, Available for download, Freely available | OMICS_01948, nlx_153893, biotools:asseq | https://bio.tools/asseq | SCR_001625 | 2026-09-19 12:49:44 | 6 | ||||||
|
GenGIS Resource Report Resource Website 10+ mentions |
GenGIS (RRID:SCR_001465) | software resource | A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. | standalone software | is listed by: OMICtools | Genome Atlantic ; Genome Canada ; Biomonitoring 2.0 Project ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation ; Natural Sciences and Engineering Research Council of Canada ; Dalhousie Faculty of Computer Science |
PMID:23922841 | Free, Available for download, Freely available | OMICS_04013 | http://kiwi.cs.dal.ca/GenGIS/ | SCR_001465 | 2026-09-19 12:49:41 | 38 | ||||||
|
ACME Resource Report Resource Website 50+ mentions |
ACME (RRID:SCR_001464) | ACME | software resource | A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. | microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:16939795 | Free, Available for download, Freely available | OMICS_01976 | SCR_001464 | Algorithms for Calculating Microarray Enrichment | 2026-09-19 12:49:41 | 62 | ||||||
|
PyLOH Resource Report Resource Website 1+ mentions |
PyLOH (RRID:SCR_001511) | software resource | Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24695406 | Free, Available for download, Freely available | OMICS_03559, biotools:pyloh | https://bio.tools/pyloh | SCR_001511 | 2026-09-19 12:49:42 | 6 | |||||||
|
CoGAPS Resource Report Resource Website 10+ mentions |
CoGAPS (RRID:SCR_001479) | CoGAPS | software resource | Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. | gene expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20810601 | Free, Available for download, Freely available | OMICS_01973 | SCR_001479 | Coordinated Gene Activity in Pattern Sets | 2026-09-19 12:49:41 | 38 | ||||||
|
Nebula Resource Report Resource Website 10+ mentions |
Nebula (RRID:SCR_001516) | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web portal that allows users to analyze ChIP-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web portal, chip-seq data, online analysis tool |
uses: Galaxy is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
PMID:22829625 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00424 | SCR_001516 | Nebula - A web-server for advanced ChIP-seq data analysis | 2026-09-19 12:49:43 | 24 | |||||||
|
ChIPseeqer Resource Report Resource Website 10+ mentions |
ChIPseeqer (RRID:SCR_001545) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that provides a comprehensive framework for the analysis of ChIP-seq data. | sequence analysis, framework, ChIP, chip-seq, chip-seq data, sequencing, data, algorithm |
is listed by: OMICtools has parent organization: Weill Cornell Medical College; New York; USA |
DOI:10.1186/1471-2105-12-277 | Free, Available for download, Freely available | OMICS_00422 | SCR_001545 | 2026-09-19 12:49:42 | 18 | ||||||||
|
flowFP Resource Report Resource Website 1+ mentions |
flowFP (RRID:SCR_001537) | software resource | A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956416 | Free, Available for download, Freely available | OMICS_05599 | SCR_001537 | flowFP - Fingerprinting for Flow Cytometry | 2026-09-19 12:49:43 | 4 | |||||||
|
MCMC.qpcr Resource Report Resource Website 10+ mentions |
MCMC.qpcr (RRID:SCR_001721) | software resource | Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977043 | Free, Available for download, Freely available | OMICS_03934 | SCR_001721 | MCMC.qpcr: Bayesian analysis of qRT-PCR data | 2026-09-19 12:49:45 | 24 | |||||||
|
rSeqDiff Resource Report Resource Website |
rSeqDiff (RRID:SCR_001683) | rSeqDiff | software resource | An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing. | rna-seq, gene expression, differential expression, differential splicing, gene |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24260225 | Free, Available for download, Freely available | OMICS_01968 | SCR_001683 | rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test | 2026-09-19 12:49:45 | 0 | ||||||
|
QuasiSeq Resource Report Resource Website 10+ mentions |
QuasiSeq (RRID:SCR_001715) | QuasiSeq | software resource | Software package to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data. | differential expression, gene, rna-seq, next generation sequencing, gene expression, mrna | is listed by: OMICtools | PMID:23104842 | Free, Available for download, Freely available | OMICS_01963 | http://cran.r-project.org/web/packages/QuasiSeq/index.html | SCR_001715 | 2026-09-19 12:49:45 | 20 | ||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | data or information resource, database, software resource | Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-09-19 12:49:46 | 0 | ||||||
|
TANGO Resource Report Resource Website 100+ mentions |
TANGO (RRID:SCR_001770) | TANGO | software resource | A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions. | polypeptide chain, polypeptide, peptide, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:15361882 | Free, Freely available | biotools:tango, OMICS_03859 | https://bio.tools/tango | SCR_001770 | 2026-09-19 12:49:46 | 136 |
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